Abstract
Accurate genotyping is essential for building genetic maps and performing genome assembly of polyploid species. Recent high-throughput techniques, such as Illumina GoldenGate™ and Sequenom iPLEX MassARRAY®, have made it possible to accurately estimate the relative abundances of different alleles even when the ploidy of the population is unknown. Here we describe the experimental methods for collecting these relative allele intensities and then demonstrate the practical concerns for inferring genotypes using Bayesian inference via the software package SuperMASSA.